Protein Protein Interaction

Question

[Plasmid]

I am new in protein interaction. I downloaded a interaction file of a protein from BioGrid database. I put this file into Cytoscape to view the interaction. In this case I only observed interaction with central protein. Is there anyway that I can get also interaction among the proteins and interaction with central protein? Are there other database that give me the same result?

Answer 1

[Pierre Lindenbaum]

The STRING Api returns all the interactions between the proteins.

eg. with eif4G1:

as XML:

http://string-db.org/api/psi-mi/interactionsList?identifiers=9606.ENSP00000316879

or as TSV:

http://string-db.org/api/psi-mi-tab/interactionsList?identifiers=9606.ENSP00000316879

Answer 2

[B. Arman Aksoy]

You can also download tab-limited dump file for HPRD directly from their website, http://www.hprd.org/download, or you can go with the Pathway Commons normalized SIF exports of various other data sources: http://www.pathwaycommons.org/pc-snapshot/current-release/sif/by_source/

These are huge 'interactome's though; Cytoscape will only build the network in the background but for visualization, you probably have to right click on the network (from the left-side menu) and use the 'create view' option explicitly.

Answer 3

[Woa]

There are some Plugins available for Cytoscape that can add interactions within the selected nodes viz. MIMI, APID2NET and BISOGENET

Cytoscape Plug-In For Retrieving Protein-Protein Interactions